Variant report

Variant	rs3130050
Chromosome Location	chr6:31618761-31618762
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:31617566..31622844-chr6:31826455..31835211,65	K562	blood:
2	chr6:31617977..31621822-chr6:31647367..31651078,5	MCF-7	breast:
3	chr6:31618484..31622073-chr6:31864833..31868659,4	K562	blood:
4	chr6:31617566..31630444-chr6:31823885..31836000,84	K562	blood:
5	chr6:31586197..31590294-chr6:31618213..31621899,10	MCF-7	breast:
6	chr6:31590485..31592545-chr6:31618288..31620102,2	MCF-7	breast:
7	chr6:31618191..31620672-chr6:31669780..31672189,2	MCF-7	breast:
8	chr6:31618325..31621676-chr6:31863690..31867276,5	K562	blood:
9	chr6:31507205..31511686-chr6:31618024..31622039,13	K562	blood:
10	chr6:31594287..31597004-chr6:31618520..31620536,2	MCF-7	breast:
11	chr6:31618645..31621732-chr6:31914935..31918984,4	K562	blood:
12	chr6:31507451..31516055-chr6:31617949..31624791,11	MCF-7	breast:
13	chr6:31461147..31462941-chr6:31618531..31620077,2	K562	blood:
14	chr6:31618346..31620951-chr6:31659194..31661993,2	MCF-7	breast:
15	chr6:31507406..31516955-chr6:31615847..31623354,26	K562	blood:
16	chr6:31512553..31516955-chr6:31618753..31622292,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000204371	Chromatin interaction
ENSG00000213760	Chromatin interaction
ENSG00000198563	Chromatin interaction
ENSG00000204498	Chromatin interaction
ENSG00000254870	Chromatin interaction
ENSG00000204386	Chromatin interaction
ENSG00000243649	Chromatin interaction
ENSG00000166278	Chromatin interaction
ENSG00000204385	Chromatin interaction
ENSG00000204469	Chromatin interaction
ENSG00000204428	Chromatin interaction
ENSG00000200816	Chromatin interaction
ENSG00000265236	Chromatin interaction
ENSG00000204427	Chromatin interaction
ENSG00000204516	Chromatin interaction
ENSG00000234006	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs2736177	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2857594	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2857600	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2857609	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2857700	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3115668	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3115669	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3117578	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130068	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3130071	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3130625	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131376	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3131377	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9267551	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv601609	chr6:31280101-31799786	Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
2	nsv601610	chr6:31280101-31960770	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	370 gene(s)	inside rSNPs	diseases
3	nsv601628	chr6:31280327-31990098	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
4	nsv601629	chr6:31280327-31996185	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
5	nsv601630	chr6:31280327-32011317	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
6	nsv601631	chr6:31280327-32017540	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
7	nsv1023939	chr6:31325961-32026747	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
8	nsv538188	chr6:31325961-32026747	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
9	nsv432868	chr6:31338844-31721033	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	250 gene(s)	inside rSNPs	diseases
10	nsv1021747	chr6:31386219-31907266	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	330 gene(s)	inside rSNPs	diseases
11	nsv830627	chr6:31496214-31659950	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
12	nsv884418	chr6:31525448-31741078	Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	206 gene(s)	inside rSNPs	diseases
13	nsv1033154	chr6:31550614-32009410	Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	326 gene(s)	inside rSNPs	diseases
14	nsv462871	chr6:31575276-31632134	Strong transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	133 gene(s)	inside rSNPs	diseases
15	nsv601942	chr6:31575276-31632134	Flanking Active TSS Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	133 gene(s)	inside rSNPs	diseases
16	nsv884419	chr6:31585000-31632651	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	138 gene(s)	inside rSNPs	diseases
17	nsv884420	chr6:31586827-31632651	Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	138 gene(s)	inside rSNPs	diseases
18	nsv884421	chr6:31588151-31631907	Active TSS Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	129 gene(s)	inside rSNPs	diseases
19	nsv884422	chr6:31592524-31631907	Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	83 gene(s)	inside rSNPs	diseases
20	nsv884424	chr6:31593729-31632651	Strong transcription Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	93 gene(s)	inside rSNPs	diseases
21	nsv1017945	chr6:31609641-32481240	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
22	esv3428142	chr6:31615800-31881809	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	257 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3130050	HLA-DRB5	cis	lymphoblastoid	seeQTL
rs3130050	HLA-C	cis	lymphoblastoid	GTEx
rs3130050	CCHCR1	Cis_1M	lymphoblastoid	RTeQTL
rs3130050	HLA-DRB5	cis	lymphoblastoid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31589800-31619400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:31590200-31618800	Strong transcription	Primary B cells from peripheral blood	blood
3	chr6:31590600-31618800	Strong transcription	Fetal Stomach	stomach
4	chr6:31590800-31618800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr6:31590800-31619000	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr6:31591400-31618800	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr6:31591600-31618800	Strong transcription	Placenta	Placenta
8	chr6:31596600-31618800	Weak transcription	Right Atrium	heart
9	chr6:31601600-31618800	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr6:31605400-31618800	Strong transcription	Fetal Muscle Trunk	muscle
11	chr6:31607400-31618800	Strong transcription	Fetal Muscle Leg	muscle
12	chr6:31616800-31619000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:31617200-31618800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr6:31617200-31619400	Weak transcription	Gastric	stomach
15	chr6:31617400-31618800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr6:31617400-31618800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr6:31617400-31618800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr6:31617400-31618800	Weak transcription	Brain Anterior Caudate	brain
19	chr6:31617400-31618800	Weak transcription	Pancreas	Pancrea
20	chr6:31617400-31619200	Weak transcription	Psoas Muscle	Psoas
21	chr6:31617600-31618800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr6:31617600-31618800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr6:31617600-31619200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr6:31617600-31619200	Weak transcription	Brain Angular Gyrus	brain
25	chr6:31617600-31619200	Weak transcription	Spleen	Spleen
26	chr6:31617600-31619400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:31617600-31619400	Weak transcription	Esophagus	oesophagus
28	chr6:31617600-31619400	Weak transcription	Ovary	ovary
29	chr6:31617600-31619400	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr6:31617600-31619600	Weak transcription	Aorta	Aorta
31	chr6:31617800-31618800	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr6:31617800-31618800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr6:31617800-31618800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr6:31617800-31618800	Weak transcription	A549	lung
35	chr6:31617800-31619000	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr6:31617800-31619000	Weak transcription	Left Ventricle	heart
37	chr6:31618000-31618800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr6:31618000-31618800	Genic enhancers	Duodenum Smooth Muscle	Duodenum
39	chr6:31618000-31618800	Genic enhancers	K562	blood
40	chr6:31618000-31619200	Genic enhancers	Primary T cells from cord blood	blood
41	chr6:31618200-31618800	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr6:31618200-31619200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr6:31618200-31619200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr6:31618400-31618800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr6:31618400-31618800	Genic enhancers	Liver	Liver
46	chr6:31618400-31618800	Enhancers	HUVEC	blood vessel
47	chr6:31618400-31619000	Genic enhancers	Primary B cells from cord blood	blood
48	chr6:31618400-31619000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
49	chr6:31618400-31619000	Weak transcription	Lung	lung
50	chr6:31618400-31619200	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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